Summary LepMap3 OrderMarkers

Pedigree: 1 wildcought female + 90 offspring (5 filtered du to low coverage (< 0.1 Mreads)) Raw data filtration: Clonefilter, ProcessRadtags. Mapping to DTOL

LepMap

ParentCall with default settings, zlimit=2 (Filtering2 with dataTolerance=)

OrderMarker, trimming and reorder using informativeMask=1 (only male informative)

## 'data.frame':    5574 obs. of  5 variables:
##  $ marker_nr    : int  5686 6205 5468 5463 6264 6206 6207 6208 6940 6462 ...
##  $ male_position: num  0 0 0 0 0 0 0 0 0 0 ...
##  $ scaffold     : Factor w/ 33 levels "LR999924.1","LR999925.1",..: 5 5 5 5 5 5 5 5 5 5 ...
##  $ position     : int  2870769 7937849 1897736 1897698 8271669 7937858 7937913 7937917 15276720 10765520 ...
##  $ lg           : int  1 1 1 1 1 1 1 1 1 1 ...
## [1] "Result from OrderMarker for: DTOL"
## [1] "Number of markers in LG: 5574"
##     lg
## 1  337
## 2  262
## 3  229
## 4  253
## 5  243
## 6  253
## 7  160
## 8  240
## 9  208
## 10 162
## 11 182
## 12 267
## 13 176
## 14 242
## 15 201
## 16 175
## 17 209
## 18 361
## 19 174
## 20 163
## 21 132
## 22  94
## 23 196
## 24 110
## 25  90
## 26 135
## 27 100
## 28  79
## 29  41
## 30  33
## 31  67
##            scaffold
## LR999924.1      354
## LR999925.1      205
## LR999926.1      248
## LR999927.1      257
## LR999928.1      336
## LR999929.1      176
## LR999930.1      193
## LR999931.1      220
## LR999932.1      203
## LR999933.1      265
## LR999934.1      170
## LR999935.1      242
## LR999936.1      248
## LR999937.1      253
## LR999938.1      206
## LR999939.1      171
## LR999940.1       30
## LR999941.1      190
## LR999942.1      243
## LR999943.1      174
## LR999944.1      143
## LR999945.1      160
## LR999946.1      138
## LR999947.1       94
## LR999948.1      103
## LR999949.1       89
## LR999950.1      155
## LR999951.1       98
## LR999952.1       79
## LR999953.1       62
## LR999954.1       32
## LR999955.1       36
## LR999956.1        1
## [1] "Map length per LG:"
##    Group.1      x
## 1        1 84.597
## 2        2 48.917
## 3        3 60.125
## 4        4 83.597
## 5        5 66.783
## 6        6 58.942
## 7        7 64.758
## 8        8 54.505
## 9        9 47.819
## 10      10 46.751
## 11      11 55.641
## 12      12 67.896
## 13      13 50.072
## 14      14 71.216
## 15      15 44.571
## 16      16 70.214
## 17      17 52.414
## 18      18 57.102
## 19      19 73.493
## 20      20 71.441
## 21      21 51.338
## 22      22 26.705
## 23      23 90.331
## 24      24 46.745
## 25      25 52.413
## 26      26 50.116
## 27      27 46.751
## 28      28 43.534
## 29      29 22.482
## 30      30 33.534
## 31      31 59.659
## [1] "Total map length: 1754.462"

library(scales)
## 
## Attaching package: 'scales'
## The following object is masked from 'package:viridis':
## 
##     viridis_pal
#V1=scaffold, V2=position, V3=lg, V4=index, V5=min_int, V6=max_int
map=read.table("mapped_int/order_int_all2.table")
head(map)
##           V1      V2 V3 V4 V5 V6
## 1 LR999928.1 7937858  1  1  0  0
## 2 LR999928.1 8009812  1  1  0  0
## 3 LR999928.1 7937849  1  1  0  0
## 4 LR999928.1 7937917  1  1  0  0
## 5 LR999928.1 7938116  1  1  0  0
## 6 LR999928.1 8271669  1  1  1  1
#summary(lm(map$V6~map$V2 + map$V1))

#plot(map[map$V1=="HiC_scaffold_19",]$V2, map[map$V1=="HiC_scaffold_19",]$V6)

#summary(lm(map$V6~map$V2 + map$V1))

NN=unique(map$V3)
MM=1
#unique(map$V4)

cl=rainbow(length(MM))


for(lg in NN) {
        print(lg)
        #png(paste0("marey", lg, ".png"))
        ymax = 0
        for (m in MM) {
                map_tmp = map[map$V3==lg & map$V4==m,]
                ymax = max(ymax, max(map_tmp$V5))
        }

        index = 1
        for (m in MM) {
                map_tmp = map[map$V3==lg & map$V4==m,]
                if (glm(map_tmp$V2 ~ map_tmp$V5)$coefficients[2] < 0) {
                        map_tmp$V5 = max(map_tmp$V5) - map_tmp$V5
                        map_tmp$V6 = max(map_tmp$V6) - map_tmp$V6
                }
                if (index == 1) {
                        plot(map_tmp$V2, map_tmp$V5, xlab="Position (Mb)",ylab="Recombination Distance",xaxt="n", main=paste0("LG", lg), col=alpha(cl[index],0.3), pch=20, cex=1.0, ylim=c(0,ymax))
                        points(map_tmp$V2, map_tmp$V6, col=alpha(cl[index],0.3), pch=20, cex=1.0)
                        arrows(map_tmp$V2, map_tmp$V5, map_tmp$V2, map_tmp$V6, length=0.0, col=alpha(cl[index],0.5),lwd=1.5)
                }
                else {
                        points(map_tmp$V2, map_tmp$V5, col=alpha(cl[index],0.3), pch=20, cex=1.0)
                        points(map_tmp$V2, map_tmp$V6, col=alpha(cl[index],0.3), pch=20, cex=1.0)
                        arrows(map_tmp$V2, map_tmp$V5, map_tmp$V2, map_tmp$V6, length=0.0, col=alpha(cl[index],0.5),lwd=1.5)
                }
                index = index + 1
        }
        #dev.off()
}
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